Installing R and RShiny on AWS
There are plenty of resources online to guide you through the process of creating an instance on AWS. Here is another one that I compiled while launching my EPI shiny app. I avoid using clients for server-laptop communication as it adds another level of confusion for me. Instead I use Terinal (macOS) and bash commands. The final script (together with other files mentioned here) can be downloaded from my github page.
Disclaimer: This is the second time I did it and I don’t have much experience with servers/shell etc, thus chances are there are mistakes and sub-optimal approaches below. Let me know if you find any and I’ll update this note.
1 Step one – Launching an Instance
1.2 AMI
Next window will prompt you to choose AMI (Amazon Machine Image). I choose Ubuntu Server 16.04 LTS (HVM), SSD Volume Type, 64-bit version. It qualifies for free tier and satisfies all my needs.
1.3 Instance type
Next window is asking for the type of the Instance. Use default and don’t press “Launch”! Instead go to “3. Configure Instance”
1.4 Disable “Auto-assign Public IP”
Here you want to disable “Auto-assign Public IP”: This would allow you to have constant IP (we will assign it later) to be associated to your instance, otherwise a new IP would be assigned every time the instance is restarted.
1.5 Security Group
Next we go to “6. Configure Security Group” and open a Shiny port (3838). The result should look like this:
1.6 Launching
Click “Review and Launch”. The review page would warn you that your instance is too open. I don’t mind that, so I go forward and press “Launch”.
1.6.1 Key pair
Now you will be prompted to create and save a key pair (security file used to connect to the server from a local machine – laptop)
Save the file in the ~/.ssh folder. Hint: use cmd+shift+G to locate the folder. Then click “Launch Instances” again. Alternatively, you could use one of the older key pair if you still have access to it.
The instance is launched. It might take some time for it to actually become active:
- pending:
- initializing:
- checked and ready for work:
2 Step two – Associating Elastic IP with the instance
AWS assigns some IP to the instance once it’s launched, and releases this IP once the instance is terminated. It might cause unwanted behaviour: As IPs are being reused you might end up having traffic causes by the previous owner of your IP. Also if you ever terminate and then relaunch an instance it would get a new IP. To avoid that you can request an Elastic IP (EIP) that would be only yours. Note though that you might be charged if you reserve an EIP but don’t associate it with any instance (not much, but still).
When we disabled “Auto-assign Public IP” option, we prevented a random IP to be assigned to our instance.
To request a new EIP, under NETWORK & SECURITY choose Elastic IPs and press “Allocate Elastic IP Address”, then press “Allocate” again.
Now you have your own Elastic IP, and you can associate it with the instance: Choose the instance and press “Associate”
And we are done with launching the server. Now we will install all the necessary software for the Shiny app on it. We will be using Terminal (I am working on macOS) and bash script to do that.
3 Step three – Installing R and RShiny
3.1 Accessing the server
Open a Terminal window and ssh to the Amazon instance (using .pem file we downloaded earlier).
(if the file is too open you might fisrt need to run “chmod 600 ./ssh newKeyPair.pem” in the terminal: This would limit the access to the file and solve the “openness”.)
Now, we are into the server:
3.2 Getting the bash script to the server
We need now to get our bash script for installing R, RShiny and fetching the app itself, to the server. I keep all that stuff on my github page, feel free to take it, modify it, reuse it, etc
First, we get the root user privileges by typing “sudo su” and then fetch the script from github using bash command “wget”. By the way, by running “man sudo” you can see the help page on the command (type “q” to exit the help page).
Now if we type “ls” we can see all the files in the current directory, that is only the file that we just uploaded. Note its color – black. It means the file is not executable and we need to change that by running “chmod +x InstallRandRShiny.sh”.
